LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
  5 = max # of 1-2 neighbors
  10 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT


neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
  1250 = # of size 2 clusters
  0 = # of size 3 clusters
  250 = # of size 4 clusters
  0 = # of frozen angles

compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude

fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse

fix fMOMENTUM all momentum 100 linear 1 1 1

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.382011
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0325934
  estimated relative force accuracy = 9.8154e-05
  using double precision FFTs
  3d grid and FFT values/proc = 103823 64000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0            0    14386.197    2910.7282    202.07402    11475.469    6565.4851    20.333365 1.0706727e-06 1.3894617e-07    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
      50     4.462481     6863.642    4633.9267    321.70512    2229.7153     735.2547     604.6946    648.35773    49.039129    824.06033    1306091.3   -1306722.9    17914.827    48631.318    504.18525 0.0086839843 
     100    8.8666639    6628.0722    4376.1868    303.81182    2251.8853    598.11249    651.43051    919.41359    74.216826     589.6504    1306135.1     -1306716    17450.721    48631.318    476.14276 0.0075129702 
     150    13.323556    6336.1884    4726.0692    328.10201    1610.1192    560.01225    621.30109    640.32475    45.531175    288.99128    1306173.9     -1306720    18303.624    48631.318    514.21215 0.0061921467 
     200    17.710109    5997.6194    4565.6288    316.96362    1431.9906     524.2765    591.79843    718.11015    56.374558    88.660843      1306183   -1306730.3    17986.182    48631.318    496.75522   0.00681205 
     250    22.154451    5648.1758    4433.1558    307.76682      1215.02    502.13687    578.85369    665.27326    49.096119   -19.019967    1306179.2   -1306740.5    11771.328    48631.318    482.34141 0.0071619539 
     300    26.524393    5317.8584    4075.2077    282.91669    1242.6506    602.55113    637.40817    647.27074    44.769726   -123.22347    1306183.3   -1306749.5    3571.1867    48631.318     443.3952 0.0071733829 
     350    30.881443     4996.709    3935.7988    273.23838    1060.9102    455.75196    634.36552    638.77826    45.831053    -157.6304    1306198.1   -1306754.3    13525.264    48631.318    428.22739 0.0063722044 
     400    35.218285    4695.9297    3742.6585    259.82983    953.27122    457.49584    620.73047    591.94411    42.495713   -183.91838    1306186.7   -1306762.2    10901.217    48631.318    407.21326  0.005787501 
     450    39.545502    4417.8027    3513.6374     243.9303    904.16528    519.61263    580.76003    624.06933    45.631271   -286.60025    1306184.3   -1306763.6    2956.9012    48631.318    382.29486 0.0057536613 
     500    43.868895    4165.0012    3333.7203    231.43976    831.28089     465.5234    579.36085    580.60005     42.34515   -254.82269    1306183.9   -1306765.6    5818.5565    48631.318    362.71904 0.0059224891 
     550    48.242395    3934.5209    3211.9362    222.98504    722.58462    431.14864    581.46511     517.2025    39.188196   -265.47041    1306182.7   -1306763.6    8537.9404    48631.318    349.46863 0.0055762504 
     600    52.542171    3714.8655    3121.0494    216.67532    593.81611    425.12998    539.89496    490.30508    34.564566   -305.82069    1306175.2   -1306765.5    7402.7677    48631.318    339.57967 0.0057486673 
     650    56.830079    3516.2452    2930.7498    203.46399    585.49537    511.91461    512.48859    521.40636    37.766801   -391.65392    1306163.5     -1306770    381.72879    48631.318    318.87447 0.0054629243 
     700    61.119511    3342.7694    2864.1576     198.8409     478.6118    451.54683    498.82407    489.17207     35.23127   -375.78886    1306153.8   -1306774.2    3691.2716    48631.318    311.62801 0.0071278731 
     750    65.401576    3181.7673    2786.7104    193.46422    395.05691    409.83192    508.19542    454.56182    32.890716   -379.80692      1306149   -1306779.6    7428.3698    48631.318    303.20195  0.006233194 
     800    69.680899    3032.4158    2699.8707    187.43547    332.54509    453.40673    486.16575     441.1235    32.847786   -437.39338    1306144.4     -1306788    1701.7652    48631.318    293.75377 0.0056528223 
     850     73.96463    2898.4928    2563.6959    177.98169     334.7969    463.66637    486.19929    453.38803    34.062233   -455.86062    1306144.2   -1306790.9   -285.03665    48631.318     278.9376 0.0052777781 
     900    78.229548    2780.3555    2528.3241    175.52604    252.03136    396.92692    451.76463    435.59744    33.035257   -413.46176    1306142.9   -1306794.7    3836.4341    48631.318    275.08801 0.0070306435 
     950    82.482848    2679.3417    2456.8817    170.56624    222.45998    385.66656     434.6516    418.37977    32.156722    -387.2201    1306136.9   -1306798.1    5510.2309    48631.318    267.31515 0.0064042654 
    1000    86.722726    2593.4365    2367.4477    164.35738    225.98882     427.8524    453.27435    415.48809    31.097577   -436.62051    1306131.8   -1306796.9    1166.3909    48631.318    257.58464 0.0059160543 
    1050    90.888482    2524.7788    2305.0253    160.02377    219.75349    432.90807    438.86657    412.79356    30.892593   -414.29436    1306119.4   -1306800.8    1698.2687    48631.318    250.79245 0.0065593259 
    1100    95.024656    2471.8176    2311.0953    160.44518    160.72227    378.43572     453.3435    392.48525    29.012472   -409.64374    1306119.6   -1306802.5      4190.91    48631.318    251.45323 0.0059713432 
    1150    99.165724    2433.9279    2279.0766    158.22231     154.8513    395.30434    436.87933    414.39389    31.118973   -428.90902    1306110.2   -1306804.2    3274.8924    48631.318    247.96893 0.0069039065 
    1200    103.31062    2411.3777    2238.4638    155.40282    172.91381    453.61551    460.27693    408.59237    31.237062   -482.78549    1306110.2   -1306808.2   -523.10179    48631.318    243.55012 0.0068754631 
    1250    107.40149    2402.1932    2286.0576    158.70696    116.13565    416.44979    462.75875    391.75373    29.446705   -477.67214    1306102.2   -1306808.8    484.04837    48631.318    248.72579  0.011679749 
    1300    111.55448    2406.5029    2261.2729    156.98631    145.23005    408.68043    437.74725     400.4567    30.448106   -418.44274    1306096.8   -1306810.5    4490.4165    48631.318    245.99228  0.076574936 
    1350    115.71244    2459.1398    2317.5855    160.89575    141.55434    651.84862    447.40877    400.66793    29.060967   -461.45124    1305884.3   -1306810.3    693.59782    48631.318    250.14098    3.5622064 
    1400    119.88515    2479.5991    2285.6701    158.68006      193.929    582.54021    457.54475    430.29254    30.183876   -449.49979    1305955.6   -1306812.8    930.31169    48631.318    247.21826    2.5935077 
    1450    124.05689    2498.3537    2286.4924    158.73715    211.86128    434.79588     477.9598    402.79356    31.070492   -406.60813    1306086.4   -1306814.5    2933.4418    48631.318    248.74646  0.058608522 
    1500    128.29115      2546.66    2423.6257    168.25747    123.03432    392.07474    456.01536    385.97457    29.255586   -417.92459    1306089.9   -1306812.3    3333.3497    48631.318      263.694  0.011243575 
    1550    132.46344    2596.5481    2325.2227    161.42596    271.32542    462.52464    469.53612    461.20308    34.616094   -423.51186    1306080.4   -1306813.4    2155.0566    48631.318    252.98739  0.011191115 
    1600    136.64497    2646.7844    2387.8797    165.77585    258.90469     424.6071    484.95314    449.56642    33.318144   -395.67454      1306077   -1306814.8    1291.5449    48631.318    259.80403  0.012426122 
    1650    140.83234    2700.2847    2387.3033    165.73584    312.98138    431.00741    496.39504    455.52303    32.724808   -357.63815    1306070.3   -1306815.3    5007.2365    48631.318    259.70198  0.081729799 
    1700    145.02103    2777.9556    2386.7756     165.6992    391.18003    636.61544    523.12627    482.84847    35.186128   -391.10505    1305919.7   -1306815.2    2192.7076    48631.318    258.14043    2.7318649 
    1750    149.22218    2829.5998    2559.2796    177.67509    270.32019      684.587    479.93609    446.30457    31.888933   -385.84966    1305832.5   -1306819.1    1683.1471    48631.318    276.95798    2.6465587 
    1800    153.41978     2835.768    2465.6959    171.17815    370.07208    470.05934    508.38934    479.71489    37.826868    -369.0767    1306062.8   -1306819.6    3023.0762    48631.318    268.22249  0.097440318 
    1850    157.62632    2857.7601    2504.3893    173.86439    353.37083    436.06841    516.10132    487.71301    36.514956   -385.43181    1306078.9   -1306816.5    2950.5189    48631.318    272.47825  0.016816883 
    1900     161.8372     2867.791    2528.8957    175.56572    338.89527    446.38065    509.27013    485.03036    37.283587   -402.68445    1306076.6   -1306812.9    3161.5045    48631.318     275.1476  0.011615474 
    1950    166.10858      2861.34    2513.9103    174.52538     347.4297     470.9855    536.84666     467.9604    36.049051   -430.05716    1306079.3   -1306813.6    738.77866    48631.318    273.51233  0.020075246 
    2000    170.32286    2838.0367    2530.4481     175.6735    307.58858    423.18694    516.91384    454.72628    35.048394   -387.67176    1306074.6   -1306809.3    4321.7103    48631.318    275.24492   0.13775419 
Loop time of 170.323 on 1 procs for 2000 steps with 5500 atoms

Performance: 0.507 ns/day, 47.312 hours/ns, 11.742 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 105.66     | 105.66     | 105.66     |   0.0 | 62.04
Bond    | 19.802     | 19.802     | 19.802     |   0.0 | 11.63
Kspace  | 35.029     | 35.029     | 35.029     |   0.0 | 20.57
Neigh   | 2.7502     | 2.7502     | 2.7502     |   0.0 |  1.61
Comm    | 0.62654    | 0.62654    | 0.62654    |   0.0 |  0.37
Output  | 0.006705   | 0.006705   | 0.006705   |   0.0 |  0.00
Modify  | 6.3072     | 6.3072     | 6.3072     |   0.0 |  3.70
Other   |            | 0.1366     |            |       |  0.08

Nlocal:    5500 ave 5500 max 5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    15407 ave 15407 max 15407 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.30509e+06 ave 1.30509e+06 max 1.30509e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1305088
Ave neighs/atom = 237.289
Ave special neighs/atom = 15.6364
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:02:50
